Buggy code:
public class Seq2c { public static void main ( String [ ] args ) throws Exception { } private static void printCoverage ( Collection < Gene > sqrlist , String covFile , boolean rewrite ) { } private static void help ( Options options ) { HelpFormatter formater = new HelpFormatter ( ) ; formater . setOptionComparator ( null ) ; <START_BUG> formater . printHelp ( 150 , ( ( Seq2c . class . getSimpleName ( ) ) + "<seq2seq4repair_space>[-options]<seq2seq4repair_space>sample2bam.txt<seq2seq4repair_space>regions.bed<seq2seq4repair_space>coverage.txt<seq2seq4repair_space>[sample_name1[:sample_name2]]\n" ) , ( "Arguments<seq2seq4repair_space>are:\n" + ( ( ( "sample2bam.txt:<seq2seq4repair_space>Required.<seq2seq4repair_space>A<seq2seq4repair_space>file<seq2seq4repair_space>containing<seq2seq4repair_space>list<seq2seq4repair_space>of<seq2seq4repair_space>samples<seq2seq4repair_space>and<seq2seq4repair_space>bam<seq2seq4repair_space>files,<seq2seq4repair_space>each<seq2seq4repair_space>sample<seq2seq4repair_space>at<seq2seq4repair_space>new<seq2seq4repair_space>line.<seq2seq4repair_space>At<seq2seq4repair_space>least<seq2seq4repair_space>two<seq2seq4repair_space>columns.<seq2seq4repair_space>\nFirst<seq2seq4repair_space>is<seq2seq4repair_space>the<seq2seq4repair_space>sample<seq2seq4repair_space>name,<seq2seq4repair_space>2nd<seq2seq4repair_space>is<seq2seq4repair_space>the<seq2seq4repair_space>bam<seq2seq4repair_space>file<seq2seq4repair_space>name.\n" + "regions.bed:<seq2seq4repair_space>Required.<seq2seq4repair_space>A<seq2seq4repair_space>bed<seq2seq4repair_space>file<seq2seq4repair_space>with<seq2seq4repair_space>regions<seq2seq4repair_space>of<seq2seq4repair_space>interest.<seq2seq4repair_space>At<seq2seq4repair_space>least<seq2seq4repair_space>4<seq2seq4repair_space>columns.\n" ) + "coverage.txt:<seq2seq4repair_space>Required.<seq2seq4repair_space>A<seq2seq4repair_space>file<seq2seq4repair_space>for<seq2seq4repair_space>writing<seq2seq4repair_space>coverage<seq2seq4repair_space>output.\n" ) + "sample_name:<seq2seq4repair_space>Control<seq2seq4repair_space>sample<seq2seq4repair_space>names.<seq2seq4repair_space>For<seq2seq4repair_space>multiple<seq2seq4repair_space>controls,<seq2seq4repair_space>separate<seq2seq4repair_space>them<seq2seq4repair_space>using<seq2seq4repair_space>\':\'.\n\n" ) ) , options , "" ) ; <END_BUG> System . exit ( 0 ) ; } private static Options buildCmdOptions ( ) { } private static int getThreadsCount ( CommandLine cmd ) throws ParseException { } public static int getRunPart ( CommandLine cmd ) throws ParseException { } }

Fix:
formater . printHelp ( 150 , ( ( Seq2c . class . getSimpleName ( ) ) + "<seq2seq4repair_space>sample2bam.txt<seq2seq4repair_space>regions.bed<seq2seq4repair_space>coverage.txt<seq2seq4repair_space>[sample_name1[:sample_name2]]<seq2seq4repair_space>[-options]\n" ) , ( "Arguments<seq2seq4repair_space>are:\n" + ( ( ( "sample2bam.txt:<seq2seq4repair_space>Required.<seq2seq4repair_space>A<seq2seq4repair_space>file<seq2seq4repair_space>containing<seq2seq4repair_space>list<seq2seq4repair_space>of<seq2seq4repair_space>samples<seq2seq4repair_space>and<seq2seq4repair_space>bam<seq2seq4repair_space>files,<seq2seq4repair_space>each<seq2seq4repair_space>sample<seq2seq4repair_space>at<seq2seq4repair_space>new<seq2seq4repair_space>line.<seq2seq4repair_space>At<seq2seq4repair_space>least<seq2seq4repair_space>two<seq2seq4repair_space>columns.<seq2seq4repair_space>\nFirst<seq2seq4repair_space>is<seq2seq4repair_space>the<seq2seq4repair_space>sample<seq2seq4repair_space>name,<seq2seq4repair_space>2nd<seq2seq4repair_space>is<seq2seq4repair_space>the<seq2seq4repair_space>bam<seq2seq4repair_space>file<seq2seq4repair_space>name.\n" + "regions.bed:<seq2seq4repair_space>Required.<seq2seq4repair_space>A<seq2seq4repair_space>bed<seq2seq4repair_space>file<seq2seq4repair_space>with<seq2seq4repair_space>regions<seq2seq4repair_space>of<seq2seq4repair_space>interest.<seq2seq4repair_space>At<seq2seq4repair_space>least<seq2seq4repair_space>4<seq2seq4repair_space>columns.\n" ) + "coverage.txt:<seq2seq4repair_space>Required.<seq2seq4repair_space>A<seq2seq4repair_space>file<seq2seq4repair_space>for<seq2seq4repair_space>writing<seq2seq4repair_space>coverage<seq2seq4repair_space>output.\n" ) + "sample_name:<seq2seq4repair_space>Control<seq2seq4repair_space>sample<seq2seq4repair_space>names.<seq2seq4repair_space>For<seq2seq4repair_space>multiple<seq2seq4repair_space>controls,<seq2seq4repair_space>separate<seq2seq4repair_space>them<seq2seq4repair_space>using<seq2seq4repair_space>\':\'.\n\n" ) ) , options , "" ) ;